MolNFT v1 · #60021 · protein
Crystal structure of purple-fluorescent antibody EP2-25C10
3CFE · Purple-fluorescent antibody EP2-25C10-kappa light chain: “Crystal structure of purple-fluorescent antibody EP2-25C10”. X-ray diffraction, 1 ligand (SO4), 11 pockets (best druggability 0.63). MolNFT v1 #60021 on GenesisL1: 3D…
- PDB
- 3CFE
- Type
- protein
- Length
- 864 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Purple-fluorescent antibody EP2-25C10-kappa light chain; Purple-fluorescent antibody…
- Ligands
- SO4
- Pockets
- 11 · best druggability 0.63
Structure
x-ray diffraction · 2 distinct chains · 5% helix, 53% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L, A | Purple-fluorescent antibody EP2-25C10-kappa light chain | protein | 213 | 6% helix, 51% strand | — |
| H, B | Purple-fluorescent antibody EP2-25C10-IGG2B heavy chain | protein | 219 | 4% helix, 55% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 5 copies · chains A, L, H, B
- GOL · Glycerol · additive · 3 copies · chains H, L, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 111 | 0.63 | 0.88 | 27 | empty |
| 2 | 109 | 0.62 | 0.87 | 24 | empty |
| 3 | 374 | 0.56 | 0.75 | 49 | empty |
| 4 | 244 | 0.51 | 0.76 | 35 | empty |
| 5 | 198 | 0.49 | 0.76 | 38 | empty |
Interfaces
2 interfaces between chains.
- L–H · 1870 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 1854 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 3CFE · Crystal structure of purple-fluorescent antibody EP2-25C10 · the same entry in another collection · chain B against B, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Elsewhere: RCSB PDB 3CFE · PDBe 3CFE
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